[Debian-med-packaging] Please check whether I fixed syntax error in proteinortho properly

[Andreas Tille]

Hi Marcus,

thanks for the effort you did to enable us to build the Debian package
properly.  I have some additional remarks:

  1. I'd recommend to strip all binaries from the source tarball.
     These should be the result of the build process.  For Debian
     we need to strip the binaries and thus the Debian source tarball
     is different from the download from your homepage which is not
     unusual but also not the prefered situation.

  2. It would be nice if you could change your Makefile in a way that
     external set CPPFLAGS and LDFLAGS are respected to propagate the
     hardening options which are usually set in Debian.  Here
      https://anonscm.debian.org/git/debian-med/proteinortho.git/tree/debian/patches/hardening.patch
     you can see, how to do this.

  3. If looking at your install target one of your build targets
     proteinortho5_tree is not mentioned in the install command.
     I suspect this is a remaining bug, right?

I have just uploaded the current state of 5.12 since it passes the
shipped test suite.  In case you might confirm and further issues I will
fix these as soon as possible.
    
Thanks a lot for your cooperation

      Andreas.

On Thu, Mar 17, 2016 at 12:59:43PM +0100, Marcus Lechner wrote:
> Hi Andreas,
> 
> thanks a lot for your feedback again. Obviously, the makefile was not
> adapted to the most recent changes in the tool. E.g. po_tree.pl needs to be
> become po2tree.pl. I have done this now and attached the full tarball with
> fixed makefile and po_tree.c. Should be fine now.
> 
> Best regards,
> Marcus
> 
> Dr. Marcus Lechner
> Bioinformatics Junior Group
> Department of Pharmaceutical Chemistry
> Philipps-University Marburg
> Marbacher Weg 6, 35037 Marburg, Germany
> Phone:  +49 (0)6421 2825925
> Mobile: +49 (0)176 38733610
> Web: http://bioinf.pharmazie.uni-marburg.de
> 
> On 03/16/2016 06:02 PM, Andreas Tille wrote:
> >Hi Marcus,
> >
> >thanks for confirming.  Unfortunately there is another build issue:
> >
> >...
> >po_tree.c:378:4: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
> >     fscanf (datei, "%c ",&(matrix[i][*ccs]));
> >     ^
> >po_tree.c:381:3: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
> >    fscanf (datei, "%c \n",&(matrix[(*viecher)-1][*ccs]));
> >    ^
> >make[2]: *** No rule to make target 'po_tree.pl', needed by 'install'.  Stop.
> >make[2]: Leaving directory '/build/proteinortho-5.12+dfsg'
> >
> >
> >Any idea from where I can get po_tree.pl?  Are you possibly some
> >repository like Github where somebody could sneak into the full source
> >that might contain pieces missing inside the tarball?
> >
> >Kind regards
> >
> >       Andreas.
> >
> >On Wed, Mar 16, 2016 at 03:18:37PM +0100, Marcus Lechner wrote:
> >>Hi Andreas,
> >>
> >>thanks a lot for your work and feedback. You've fixed the error correctly (/
> >>need be be removed). I'll merge this in the next version of Proteinortho.
> >>
> >>Best regards,
> >>Marcus
> >>
> >>Dr. Marcus Lechner
> >>Bioinformatics Junior Group
> >>Department of Pharmaceutical Chemistry
> >>Philipps-University Marburg
> >>Marbacher Weg 6, 35037 Marburg, Germany
> >>Phone:  +49 (0)6421 2825925
> >>Mobile: +49 (0)176 38733610
> >>Web: http://bioinf.pharmazie.uni-marburg.de
> >>
> >>On 03/16/2016 02:09 PM, Andreas Tille wrote:
> >>>Hi Marcus,
> >>>
> >>>I'm not sure whether it becomes clear that the last release of
> >>>proteinortho (5.12) has a serious syntax error which makes the build
> >>>fail.  The patch below fixes the syntax issue but I'm not 100% sure
> >>>whether it is correct in terms of content.
> >>>
> >>>Please check your code accordingly.
> >>>
> >>>Kind regards
> >>>
> >>>      Andreas
> >>>
> >>>On Thu, Mar 10, 2016 at 08:57:55PM +0100, Andreas Tille wrote:
> >>>>Hi Marcus,
> >>>>
> >>>>when trying to upgrade proteinortho Debian package to version 5.12 I
> >>>>faced a syntax error which is most probably a typo.  Please verify
> >>>>that the intention was to *remove* the comment sign as I did in this
> >>>>patch:
> >>>>
> >>>>     https://anonscm.debian.org/cgit/debian-med/proteinortho.git/tree/debian/patches/fix_syntax.patch
> >>>>
> >>>>Kind regards
> >>>>
> >>>>       Andreas.
> >>>>
> >>>>-- 
> >>>>http://fam-tille.de
> >>
> 



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